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LIMS-759: Show multipin samples and their sublocations
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Mark Williams committed Aug 22, 2023
1 parent e8c96c8 commit 2003205
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Showing 6 changed files with 57 additions and 36 deletions.
2 changes: 1 addition & 1 deletion api/src/Page/Sample.php
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Original file line number Diff line number Diff line change
Expand Up @@ -1151,7 +1151,7 @@ function _samples()
$order = $cols[$this->arg('sort_by')] . ' ' . $dir;
}

$rows = $this->db->paginate("SELECT distinct b.blsampleid, b.crystalid, b.screencomponentgroupid, ssp.blsampleid as parentsampleid, ssp.name as parentsample, b.blsubsampleid, count(distinct si.blsampleimageid) as inspections, CONCAT(p.proposalcode,p.proposalnumber) as prop, b.code, b.location, pr.acronym, pr.proteinid, cr.spacegroup,b.comments,b.name,s.shippingname as shipment,s.shippingid,d.dewarid,d.code as dewar, c.code as container, c.containerid, c.samplechangerlocation as sclocation, count(distinct IF(dc.overlap != 0,dc.datacollectionid,NULL)) as sc, count(distinct IF(dc.overlap = 0 AND dc.axisrange = 0,dc.datacollectionid,NULL)) as gr, count(distinct IF(dc.overlap = 0 AND dc.axisrange > 0,dc.datacollectionid,NULL)) as dc, count(distinct IF(dcg.experimenttype LIKE 'XRF map', dc.datacollectionid, NULL)) as xm, count(distinct IF(dcg.experimenttype LIKE 'XRF spectrum', dc.datacollectionid, NULL)) as xs, count(distinct IF(dcg.experimenttype LIKE 'Energy scan', dc.datacollectionid, NULL)) as es, count(distinct so.screeningid) as ai, count(distinct app.autoprocprogramid) as ap, count(distinct r.robotactionid) as r, round(min(st.rankingresolution),2) as scresolution, max(ssw.completeness) as sccompleteness, round(min(apss.resolutionlimithigh),2) as dcresolution, round(max(apss.completeness),1) as dccompleteness, dp.anomalousscatterer, dp.requiredresolution, cr.cell_a, cr.cell_b, cr.cell_c, cr.cell_alpha, cr.cell_beta, cr.cell_gamma, b.packingfraction, b.dimension1, b.dimension2, b.dimension3, b.shape, cr.color, cr.theoreticaldensity, cr.name as crystal, pr.name as protein, b.looptype, dp.centringmethod, dp.experimentkind, cq.containerqueueid, TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp
$rows = $this->db->paginate("SELECT distinct b.blsampleid, b.crystalid, b.screencomponentgroupid, ssp.blsampleid as parentsampleid, ssp.name as parentsample, b.blsubsampleid, count(distinct si.blsampleimageid) as inspections, CONCAT(p.proposalcode,p.proposalnumber) as prop, b.code, b.location, b.sublocation, pr.acronym, pr.proteinid, cr.spacegroup,b.comments,b.name,s.shippingname as shipment,s.shippingid,d.dewarid,d.code as dewar, c.code as container, c.containerid, c.samplechangerlocation as sclocation, count(distinct IF(dc.overlap != 0,dc.datacollectionid,NULL)) as sc, count(distinct IF(dc.overlap = 0 AND dc.axisrange = 0,dc.datacollectionid,NULL)) as gr, count(distinct IF(dc.overlap = 0 AND dc.axisrange > 0,dc.datacollectionid,NULL)) as dc, count(distinct IF(dcg.experimenttype LIKE 'XRF map', dc.datacollectionid, NULL)) as xm, count(distinct IF(dcg.experimenttype LIKE 'XRF spectrum', dc.datacollectionid, NULL)) as xs, count(distinct IF(dcg.experimenttype LIKE 'Energy scan', dc.datacollectionid, NULL)) as es, count(distinct so.screeningid) as ai, count(distinct app.autoprocprogramid) as ap, count(distinct r.robotactionid) as r, round(min(st.rankingresolution),2) as scresolution, max(ssw.completeness) as sccompleteness, round(min(apss.resolutionlimithigh),2) as dcresolution, round(max(apss.completeness),1) as dccompleteness, dp.anomalousscatterer, dp.requiredresolution, cr.cell_a, cr.cell_b, cr.cell_c, cr.cell_alpha, cr.cell_beta, cr.cell_gamma, b.packingfraction, b.dimension1, b.dimension2, b.dimension3, b.shape, cr.color, cr.theoreticaldensity, cr.name as crystal, pr.name as protein, b.looptype, dp.centringmethod, dp.experimentkind, cq.containerqueueid, TO_CHAR(cq.createdtimestamp, 'DD-MM-YYYY HH24:MI') as queuedtimestamp
, $cseq $sseq string_agg(cpr.name) as componentnames, string_agg(cpr.density) as componentdensities
,string_agg(cpr.proteinid) as componentids, string_agg(cpr.acronym) as componentacronyms, string_agg(cpr.global) as componentglobals, string_agg(chc.abundance) as componentamounts, string_agg(ct.symbol) as componenttypesymbols, b.volume, pct.symbol,ROUND(cr.abundance,3) as abundance, TO_CHAR(b.recordtimestamp, 'DD-MM-YYYY') as recordtimestamp, dp.radiationsensitivity, dp.energy, dp.userpath, dp.strategyoption, dp.minimalresolution as minimumresolution
,count(distinct dc.dataCollectionId) as dcc
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25 changes: 17 additions & 8 deletions client/src/js/app/store/modules/store.samples.js
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ const INITIAL_SAMPLE_STATE = {
SAMPLEGROUP: '',
INITIALSAMPLEGROUP: '',
STATUS: '',
SUBLOCATION: null,
}

// Use Location as idAttribute for this table
Expand Down Expand Up @@ -95,26 +96,35 @@ const samplesModule = {
setSample(state, { data, index }) {
if (index < state.samples.length) state.samples.splice(index, 1, data)
},
// For each sample put it in the correct place, based on location, in the capacity array
// For each sample put it in the correct place, based on location & sublocation, in the capacity array
setAllSamples(state, {capacity, samples}) {

const state_samples = Array.from({ length: capacity }, (_, i) => new LocationSample({
const state_samples = Array.from({ length: capacity*10 }, (_, i) => new LocationSample({
BLSAMPLEID: null,
LOCATION: (i + 1).toString(),
LOCATION: (parseInt(i/10) + 1).toString(),
INDEX: i,
PROTEINID: -1,
CRYSTALID: -1,
new: true
}))

if (samples) {
for (let sample of samples) {
const index = Number(sample.LOCATION)-1
if (index < capacity) {
const index = 10*(Number(sample.LOCATION)-1)+Number(sample.SUBLOCATION)
sample.INDEX = index
if (index < capacity*10) {
state_samples[index] = sample
}
}
}
state.samplesCollection.reset(state_samples)
state.samples = state.samplesCollection.toJSON().filter(() => { return true })
state.samples = state.samplesCollection.toJSON().filter(function(e, i, a) {
if (e.BLSAMPLEID) { return true }
for (var j of a) {
if (j.BLSAMPLEID && j.LOCATION === e.LOCATION) { return false }
}
return true
})
},
clearSample(state, index) {
if (index < state.samples.length) state.samples.splice(index, 1, {
Expand Down Expand Up @@ -156,7 +166,7 @@ const samplesModule = {
// Convert our samples json to a backbone collection
state.samples.map(s => {
s.CONTAINERID = containerId
let locationIndex = +(s.LOCATION - 1)
let locationIndex = +s.INDEX
let proteinId = +s.PROTEINID
if (proteinId > 0 && s.NAME !== '') {
state.samplesCollection.at(locationIndex).set(s)
Expand All @@ -174,7 +184,6 @@ const samplesModule = {
const oldSamplesCollection = new Samples()

state.samples.forEach(sample => {
// const locationIndex = +sample['LOCATION'] - 1
if (sample['PROTEINID'] && sample['NAME'] && sample['BLSAMPLEID']) {
oldSamplesCollection.add(sample)
}
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7 changes: 6 additions & 1 deletion client/src/js/modules/types/mx/samples/mx-puck-samples-table.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -188,6 +188,11 @@ export default {
title: 'Loc',
className: 'location-column'
},
{
key: 'SUBLOCATION',
title: 'Sub',
className: 'sublocation-column'
},
{
key: 'ACRONYM',
title: 'Protein Acronym',
Expand Down Expand Up @@ -542,4 +547,4 @@ export default {
.min-height-8 {
min-height: 32px;
}
</style>
</style>
2 changes: 1 addition & 1 deletion client/src/js/modules/types/mx/samples/sample-table-mixin.js
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Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ export default {
editRow(row) {
this.editingSample = row;
this.editingSample.CONTAINERID = this.containerId;
this.$emit('update-editing-row', row.LOCATION)
this.$emit('update-editing-row', row.INDEX)
},
formatSelectData(selectData, data, property) {
const matchedSelectData = selectData.find(select => select.value === data[property])
Expand Down
19 changes: 13 additions & 6 deletions client/src/js/modules/types/mx/samples/sample-table-row.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,21 @@
{{ sample.LOCATION || sampleIndex + 1 }}
</div>

<div class="sublocation-column tw-text-center tw-py-1">
{{ sample.SUBLOCATION }}
</div>

<validation-provider
v-slot="{ errors }"
class="tw-px-2 protein-column tw-py-1"
tag="div"
:rules="sample['NAME'] && (!containerId || editingRow === sample['LOCATION']) ? 'required' : ''"
:rules="sample['NAME'] && (!containerId || editingRow === sample['INDEX']) ? 'required' : ''"
:name="`Sample ${sampleIndex + 1} Protein`"
:vid="`sample ${sampleIndex + 1} protein`"
>
<combo-box
v-model="PROTEINID"
:is-disabled="!canEditRow(sample['LOCATION'], editingRow) || isContainerProcessing || sampleHasDataCollection"
:is-disabled="!canEditRow(sample['INDEX'], editingRow) || isContainerProcessing || sampleHasDataCollection"
:data="proteinsOptionsList"
class="tw-w-full protein-select"
dataTestId="add-container-protein-select"
Expand Down Expand Up @@ -50,12 +54,12 @@
v-slot="{ errors }"
tag="div"
class="name-column tw-py-1 tw-px-2"
:rules="sample['PROTEINID'] > -1 && (!containerId || editingRow === sample['LOCATION']) ? 'required|alpha_dash|max:25|' : ''"
:rules="sample['PROTEINID'] > -1 && (!containerId || editingRow === sample['INDEX']) ? 'required|alpha_dash|max:25|' : ''"
:name="`Sample ${sampleIndex + 1} Name`"
:vid="`sample ${sampleIndex + 1} name`"
>
<base-input-text
:disabled="!canEditRow(sample['LOCATION'], editingRow) || isContainerProcessing || sampleHasDataCollection"
:disabled="!canEditRow(sample['INDEX'], editingRow) || isContainerProcessing || sampleHasDataCollection"
v-model.trim="NAME"
input-class="tw-w-full tw-h-8"
:error-message="errors[0]"
Expand All @@ -75,7 +79,7 @@
<template #default="{ errors, inputChanged }">
<combo-box
v-model="SAMPLEGROUP"
:is-disabled="!canEditRow(sample['LOCATION'], editingRow) || sampleGroupInputDisabled"
:is-disabled="!canEditRow(sample['INDEX'], editingRow) || sampleGroupInputDisabled"
:data="sampleGroups"
text-field="text"
value-field="value"
Expand All @@ -102,7 +106,7 @@

<div class="actions-column tw-py-1 tw-text-right">
<span v-if="containerId">
<span v-if="editingRow === sample['LOCATION']">
<span v-if="editingRow === sample['INDEX']">
<a
class="button tw-cursor-pointer "
@click="$emit('save-sample', sampleIndex)"
Expand Down Expand Up @@ -214,6 +218,9 @@ export default {
.location-column {
width: 30px;
}
.sublocation-column {
width: 30px;
}
.protein-column {
width: 15%;
}
Expand Down
38 changes: 19 additions & 19 deletions client/src/js/modules/types/mx/samples/tabbed-columns-view.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
<template #default="{ errors, inputChanged }">
<base-input-select
v-model="ANOMALOUSSCATTERER"
:is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:is-disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
:options="anomalousOptionsList"
input-class="tw-w-full tw-h-8"
option-value-key="value"
Expand All @@ -36,7 +36,7 @@
<template #default="{ errors, inputChanged }">
<base-input-text
v-model="CODE"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
input-class="tw-w-full tw-h-8"
@value-changed="inputChanged"
/>
Expand All @@ -52,7 +52,7 @@
<template #default="{ errors, inputChanged }">
<base-input-text
v-model="COMMENTS"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
input-class="tw-w-full tw-h-8"
@value-changed="inputChanged"
dataTestId="add-container-sample-comment"
Expand Down Expand Up @@ -89,7 +89,7 @@
<template #default="{ errors, inputChanged }">
<base-input-text
v-model="USERPATH"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
input-class="tw-w-full tw-h-8"
:error-message="errors[0]"
:quiet="true"
Expand All @@ -108,7 +108,7 @@
<template #default="{errors, inputChanged}">
<base-input-select
v-model="SPACEGROUP"
:is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:is-disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
:options="spaceGroupList"
option-value-key="value"
option-text-key="text"
Expand All @@ -134,7 +134,7 @@
<template #default="{errors, inputChanged}">
<base-input-text
v-model="CELL_A"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
placeholder-text="A"
:quiet="true"
type="number"
Expand All @@ -157,7 +157,7 @@
<template #default="{ errors, inputChanged }">
<base-input-text
v-model="CELL_B"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
placeholder-text="B"
:quiet="true"
type="number"
Expand All @@ -180,7 +180,7 @@
<template #default="{errors, inputChanged}">
<base-input-text
v-model="CELL_C"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
placeholder-text="C"
input-class="tw-w-12 tw-h-8 tabbed-sample-column"
type="number"
Expand All @@ -206,7 +206,7 @@
<template #default="{errors, inputChanged}">
<base-input-text
v-model="CELL_ALPHA"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
placeholder-text="α"
input-class="tw-w-12 tw-h-8 tabbed-sample-column"
:quiet="true"
Expand All @@ -229,7 +229,7 @@
<template #default="{ errors, inputChanged }">
<base-input-text
v-model="CELL_BETA"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
placeholder-text="β"
input-class="tw-w-12 tw-h-8 tabbed-sample-column"
type="number"
Expand All @@ -252,7 +252,7 @@
<template #default="{errors, inputChanged}">
<base-input-text
v-model="CELL_GAMMA"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
placeholder-text="γ"
input-class="tw-w-12 tw-h-8 tabbed-sample-column"
type="number"
Expand Down Expand Up @@ -282,7 +282,7 @@
<template #default="{errors, inputChanged }">
<base-input-select
v-model="CENTRINGMETHOD"
:is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:is-disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
:options="centringMethodList"
option-value-key="value"
option-text-key="text"
Expand All @@ -305,7 +305,7 @@
<template #default="{errors, inputChanged}">
<base-input-select
v-model="EXPERIMENTKIND"
:is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:is-disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
:options="experimentKindList"
input-class="tw-w-full tw-h-8"
option-value-key="value"
Expand All @@ -328,7 +328,7 @@
<template #default="{errors, inputChanged }">
<base-input-text
v-model="ENERGY"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
input-class="tw-w-full tw-h-8 tabbed-sample-column"
type="number"
:step="1"
Expand All @@ -350,7 +350,7 @@
<template #default="{ errors, inputChanged }">
<base-input-select
v-model="ANOMALOUSSCATTERER"
:is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:is-disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
:options="anomalousOptionsList"
option-value-key="value"
input-class="tw-w-full tw-h-8"
Expand All @@ -372,7 +372,7 @@
<template #default="{ errors, inputChanged }">
<base-input-select
v-model="SCREENINGMETHOD"
:is-disabled="!canEditRow(sample['LOCATION'], currentEditingRow)"
:is-disabled="!canEditRow(sample['INDEX'], currentEditingRow)"
:options="screeningMethodList"
option-value-key="value"
option-text-key="text"
Expand All @@ -395,7 +395,7 @@
<template #default="{ errors, inputChanged}">
<base-input-text
v-model="REQUIREDRESOLUTION"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow) || sample['SCREENINGMETHOD'] !== 'none'"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow) || sample['SCREENINGMETHOD'] !== 'none'"
type="number"
:step="1"
input-class="tw-w-full tw-h-8 tabbed-sample-column"
Expand All @@ -417,7 +417,7 @@
<template #default="{ errors, inputChanged }">
<base-input-text
v-model="MINIMUMRESOLUTION"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow) || sample['SCREENINGMETHOD'] !== 'all'"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow) || sample['SCREENINGMETHOD'] !== 'all'"
type="number"
:step="1"
input-class="tw-w-full tw-h-8 tabbed-sample-column"
Expand All @@ -439,7 +439,7 @@
<template #default="{ errors, inputChanged}">
<base-input-text
v-model="SCREENINGCOLLECTVALUE"
:disabled="!canEditRow(sample['LOCATION'], currentEditingRow) || sample['SCREENINGMETHOD'] !== 'best'"
:disabled="!canEditRow(sample['INDEX'], currentEditingRow) || sample['SCREENINGMETHOD'] !== 'best'"
type="number"
:step="1"
input-class="tw-w-full tw-h-8 tabbed-sample-column"
Expand Down

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